International Graduate School in Bioinformatics and Genome Research, Center for Biotechnology, Bielefeld, Germany

BMC Bioinformatics 2007, 8:429
doi:10.1186/1471-2105-8-429

Published: 6 November 2007

Abstract

Background

Detailed information on DNA-binding transcription factors (the key players in the
regulation of gene expression) and on transcriptional regulatory interactions of microorganisms
deduced from literature-derived knowledge, computer predictions and global DNA microarray
hybridization experiments, has opened the way for the genome-wide analysis of transcriptional
regulatory networks. The large-scale reconstruction of these networks allows the in
silico analysis of cell behavior in response to changing environmental conditions.
We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial
transcription factors and regulatory networks. Initially, it was designed to provide
methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum.

Results

Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory
networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access
the database content, to allow various queries, and to support the reconstruction,
analysis and visualization of regulatory networks at different hierarchical levels.
In this article, we present the further improved database content of CoryneRegNet
along with novel analysis features. The network visualization feature GraphVis now
allows the inter-species comparisons of reconstructed gene regulatory networks and
the projection of gene expression levels onto that networks. Therefore, we added stimulon
data directly into the database, but also provide Web Service access to the DNA microarray
analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service
server, which can easily be consumed by other bioinformatics software systems. Stimulons
(imported from the database, or uploaded by the user) can be analyzed in the context
of known transcriptional regulatory networks to predict putative contradictions or
further gene regulatory interactions. Furthermore, it integrates protein clusters
by means of heuristically solving the weighted graph cluster editing problem. In addition,
it provides Web Service based access to up to date gene annotation data from GenDB.

Conclusion

The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis
of procaryotic gene regulatory networks. It is a versatile systems biology platform
to support the efficient and large-scale analysis of transcriptional regulation of
gene expression in microorganisms. It is publicly available at http://www.CoryneRegNet.DEwebcite.